load_cluster_data <- function(from_scratch=FALSE) {
if (!from_scratch) {
cluster_result <- readRDS(system.file("extdata", "cluster_result.rds", package = "RichCluster"))
} else {
rr1 <- read.delim(system.file("extdata", "go1.txt", package = "RichCluster"))
rr2 <- read.delim(system.file("extdata", "go2.txt", package = "RichCluster"))
enrichment_results <- list(rr1, rr2)
rr_names <- c('7mo_DEG', '7mo_DMR')
cluster_result <- RichCluster::cluster(
enrichment_results, df_names = rr_names, min_terms = 5,
distance_metric = "kappa", distance_cutoff = 0.5,
linkage_method = "average", linkage_cutoff = 0.5
)
}
return(cluster_result)
}
cluster_result <- load_cluster_data(from_scratch = FALSE)c_hmap <- cluster_hmap(cluster_result)
#> Warning in fix_not_all_unique(rownames(x)): Not all the values are unique - manually added prefix numbers
c_hmapclusters <- c("mating plug formation", "regulation of protein refolding", "regulation of plasma cell differentiation")
terms <- c("neuroblast proliferation", "regulation of tissue remodeling", "protein secretion")
t_hmap <- term_hmap(cluster_result, clusters, terms, value_type = "Padj")
#> [1] "-log10(Padj)"
t_hmapcluster_df <- export_df(cluster_result)
head(cluster_df)
#> Cluster ClusterName
#> 1 1 skeletal muscle cell differentiation
#> 2 1 skeletal muscle cell differentiation
#> 3 1 skeletal muscle cell differentiation
#> 4 1 skeletal muscle cell differentiation
#> 5 1 skeletal muscle cell differentiation
#> 6 1 skeletal muscle cell differentiation
#> Term Annot_7mo_DEG Annotated_7mo_DEG
#> 1 regulation of cellular senescence GO:2000772 27
#> 2 skeletal muscle organ development GO:0060538 195
#> 3 cellular response to oxidative stress GO:0034599 233
#> 4 type B pancreatic cell development GO:0003323 21
#> 5 negative regulation of intracellular steroid hormone receptor signaling pathway GO:0033144 32
#> 6 regulation of cell aging GO:0090342 34
#> Significant_7mo_DEG Pvalue_7mo_DEG Padj_7mo_DEG GeneID_7mo_DEG Annot_7mo_DMR Annotated_7mo_DMR Significant_7mo_DMR
#> 1 1 0.02727905 0.11680502 Arntl <NA> NA NA
#> 2 2 0.01683191 0.09358109 Arntl,Ankrd2 <NA> NA NA
#> 3 2 0.02349213 0.11116047 Arntl,Ankrd2 <NA> NA NA
#> 4 1 0.02127938 0.10351325 Arntl <NA> NA NA
#> 5 1 0.03225184 0.12253346 Arntl <NA> NA NA
#> 6 1 0.03423413 0.12592837 Arntl <NA> NA NA
#> Pvalue_7mo_DMR Padj_7mo_DMR GeneID_7mo_DMR GeneID Pvalue Padj
#> 1 NA NA <NA> Arntl 0.02727905 0.11680502
#> 2 NA NA <NA> Arntl,Ankrd2 0.01683191 0.09358109
#> 3 NA NA <NA> Arntl,Ankrd2 0.02349213 0.11116047
#> 4 NA NA <NA> Arntl 0.02127938 0.10351325
#> 5 NA NA <NA> Arntl 0.03225184 0.12253346
#> 6 NA NA <NA> Arntl 0.03423413 0.12592837